Print Email Facebook Twitter High-Performance and Scalable Agent-Based Simulation with BioDynaMo Title High-Performance and Scalable Agent-Based Simulation with BioDynaMo Author Breitwieser, Lukas (CERN; ETH Zürich) Hesam, A.S. (TU Delft Computer Engineering) Rademakers, Fons (CERN) Luna, Juan Gómez (ETH Zürich) Mutlu, Onur (ETH Zürich) Date 2023 Abstract Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low performance of the underlying simulation engines. To overcome this limitation, we present a novel high-performance simulation engine. We identify three key challenges for which we present the following solutions. First, to maximize parallelization, we present an optimized grid to search for neighbors and parallelize the merging of thread-local results. Second, we reduce the memory access latency with a NUMA-aware agent iterator, agent sorting with a space-filling curve, and a custom heap memory allocator. Third, we present a mechanism to omit the collision force calculation under certain conditions. Our evaluation shows an order of magnitude improvement over Biocellion, three orders of magnitude speedup over Cortex3D and NetLogo, and the ability to simulate 1.72 billion agents on a single server. Supplementary Materials, including instructions to reproduce the results, are available at: https://doi.org/10.5281/zenodo.6463816 Subject agent-based modelinghigh-performance simulationHPCmemory allocationmemory layout optimizationNUMAparallel computingperformance evaluationperformance optimizationscalabilityspace-filling curve To reference this document use: http://resolver.tudelft.nl/uuid:8c6308eb-3817-4260-a590-e8dd10a853ed DOI https://doi.org/10.1145/3572848.3577480 Publisher Association for Computing Machinery (ACM) ISBN 979-8-4007-0015-6 Source PPoPP 2023 - Proceedings of the 28th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming Event 28th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming, PPoPP 2023, 2023-02-25 → 2023-03-01, Montreal, Canada Series Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP Part of collection Institutional Repository Document type conference paper Rights © 2023 Lukas Breitwieser, A.S. Hesam, Fons Rademakers, Juan Gómez Luna, Onur Mutlu Files PDF 3572848.3577480.pdf 4.41 MB Close viewer /islandora/object/uuid:8c6308eb-3817-4260-a590-e8dd10a853ed/datastream/OBJ/view